Ontology meeting 2015-04-16
Attendees:Rama, Harold, DavidOS, Paola, Rama, Heiko, DavidH, PaulT
Minutes: DavidH
Prefixing of obsolete to label of all obsoletes
We should really do this for consistency. Or alternately remove from the release version since they are primarily there for the edit cycle.
Consensus is we should be consistent and just prepend all the obsolete terms with obsolete-. The tag will still remain.
ORE 2015 (not covered)
We should enter GO for this year's OWL reasoner evaluation competition. DOS: I'll enter go-plus.owl, but would also like to enter this combined with an annotation set expressed as OWL along with some queries across data. Can we get this ready for May 1st?
Follow-up: qualifier for (regulation of process or process)
Copying from last week - we need to discuss more today, and Rama will join us:
(For background, see http://wiki.geneontology.org/index.php/Ontology_meeting_2015-04-02)
It was suggested to discuss this at a managers' call first, and then at an annotation call. Also, the issue was raised that there needs to be complete alignment from all parts (curators + editors) on what we mean by direct vs indirect regulation.
If DNA replication doesn't happen, cell division doesn't happen. However one doesn't want to say that DNA replication regulates cell division. Val enumerated three cases where the new qualifier could be used. New qualifier was supposed to be very clear semantically = (BP + RofBP). Not cover the fuzzy, I don't know approach - I don't know if it's part of the process or regulates the process or is not involved! May need to drop this qualifier. Problem annotations: embryo development IMP because of embryo lethality - are those gps really involved in embryogenesis?
'implicated in' meant to be a hedge for process + indirectly/directly regulation
of process NOT ("affected by" but not necessarily via a regulatory mechanism) but
doesn't seem to map to the hedge that people want to make (where they don't know)
Need broader discussion with annotation group, can't solve only in ontology group. Pretend that we made this qualifier and record when we would use it, discuss in annotation call? Collect information and bring to GOC meeting? How about something more top down? Maybe one can enumerate the possibilities in greater detail. Push to discussion again next week.
If we bring in the qualifier, will we tempt people to annotate where they wouldn't have annotated. Do we create a fuzzy relationship that means part_of, regulates, upstream_of? We think this might be a good way to go. Action plan is to make this more formal, then to present to the annotation group.
TermGenie access for students
Jim Hu (a few weeks ago) and Ruth both have students who wish to create a new class with TermGenie. From a technical perspective giving access to them is easy.
But so far every submitter has also been assigned a GOC reference. I do not know if it would be a good policy to introduce this for students too.
Ideas:
- Use the GOC ref of their supervisor to have a permanent record.
- Create a common GOC for the students of on institution (one for UT A&M students, one for UCL students)
- Other ideas?
Update: Paola has already created individual GOC refs for the UCL students. So I assume that the overall number is not an issue.
They will get access just to the templated form. The free-form is completely separate.
Regulation of gene expression levels
Solution needed ASAP for Rachael/Ruth
Background: The annotation extension pattern 'regulation of gene expression' that has_regulation_target some fu is, apparently, frequently used for cases of where annotators are not comfortable that they can infer regulation of process that come under GO gene expression (transcription, translation, maturation) of the target gene - as distinct from regulation of levels of a gene product, which might arise from regulation of degradation of that gene product. Rachael also has a specific use case for miRNA where target RNA modification either regulates translation or leads to target RNA degradation. Based on discussion of this, we previously, provisionally agreed to add a term for regulation of gene expression levels, defined as regulation of a quality (level of a gene product) rather than of the process 'gene expression'. This would be combined in annotation with a new, specific relation (regulates_levels_of_product_of ?).
Rachael asks: how will the new GO class “regulation of gene expression levels” relate to the current “regulation of gene expression” - will it replace it or be a parent? I think I need to see how it will fit into the current ontology to see what it covers.
Get rid of the existing term? Merge? May be better than an obsoletion and replaced_by. Or are the types of experiments being described here actually phenotypes? 942 annotations directly to reg of gene expression. Somehow we want to capture the main point of the biology. We want to somehow capture the specificity of the regulation.
Axiomatizing Regulation of Biological Quality (not covered)
Any objections to Chris' suggestion of going ahead and adding?
DOS: Mostly looks good. Not sure about location pattern though. occurs_in definition has domain process (although this is not formalised).
Details on email thread with same title on ontology list:
David H and I have gone through the proposed logical defs for RoBQs
http://wiki.geneontology.org/index.php/Extensions/x-attribute
(the wiki is v out of date, but these extension pages can soon disappear once is everything is part of the normal edit cycle)
These make use of OBA, which you can find out more about here:
https://github.com/obophenotype/bio-attribute-ontology/
including links to the OBA TG etc
I think they are now all valid (completeness can wait). I propose just going ahead and adding, raise any objections on thursday call
(Transmembrane) transport templates in TG (not covered)
See email thread "Transmembrane transport again..." started by Paola on April 10th. Please comment.
Generic pattern in ontology:
transport/import/export
and ('has target start location' some A
and ('has target end location' some B)
and (imports some C)
and ('results_in_transport_across some D)
Should/could we implement this as a general TG template, or are more specific ones more appropriate?
New TG templates (not covered)
Punted from last week:
The job of editors on SF and TG duties would benefit considerably if we could implement some TG functionalities we've already sort of agreed upon. We may want to revisit the related requests, prioritize, see what's missing.
1) TG: create MF-BP links when appropriate https://www.ebi.ac.uk/panda/jira/browse/GO-199
2) Create TermGenie templates with UBERON https://www.ebi.ac.uk/panda/jira/browse/GO-168 - follow-up
Last week we wrote:
May be done already. Chris and Heiko will look into this. Something is still missing. There was a problem with propagation over 'part_of' in the anatomy ontology and that extending into the GO ontology, development -- morphogenesis. May be not urgent at this time. Wait for requests to come in and then roll out the template. Code is mostly in place but not switched on. Need to deal with the part_of thing before rolling out.
A non-development request to add a part_of link that could have been inferred automatically: https://sourceforge.net/p/geneontology/ontology-requests/11635/
3) TG template for 'cellular component organization' https://www.ebi.ac.uk/panda/jira/browse/GO-327
4) TG template for 'cellular component binding' https://www.ebi.ac.uk/panda/jira/browse/GO-326
5) Create term genie template for response to organism https://www.ebi.ac.uk/panda/jira/browse/GO-212
GO-UBERON issues (not covered)
If DavidOS is back can we discuss Stan's hindgut issue and the issue of multi-species fuzziness in general?